Job ID = 6627515 SRX = SRX8521337 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:45 42501714 reads; of these: 42501714 (100.00%) were unpaired; of these: 34298701 (80.70%) aligned 0 times 6316858 (14.86%) aligned exactly 1 time 1886155 (4.44%) aligned >1 times 19.30% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 1318203 / 8203013 = 0.1607 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 11:54:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 11:54:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:54:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:54:58: 1000000 INFO @ Tue, 14 Jul 2020 11:55:04: 2000000 INFO @ Tue, 14 Jul 2020 11:55:09: 3000000 INFO @ Tue, 14 Jul 2020 11:55:15: 4000000 INFO @ Tue, 14 Jul 2020 11:55:20: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 11:55:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 11:55:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:55:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:55:26: 6000000 INFO @ Tue, 14 Jul 2020 11:55:29: 1000000 INFO @ Tue, 14 Jul 2020 11:55:31: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 11:55:31: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 11:55:31: #1 total tags in treatment: 6884810 INFO @ Tue, 14 Jul 2020 11:55:31: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:55:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:55:31: #1 tags after filtering in treatment: 6884628 INFO @ Tue, 14 Jul 2020 11:55:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:55:31: #1 finished! INFO @ Tue, 14 Jul 2020 11:55:31: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:55:32: #2 number of paired peaks: 526 WARNING @ Tue, 14 Jul 2020 11:55:32: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Tue, 14 Jul 2020 11:55:32: start model_add_line... INFO @ Tue, 14 Jul 2020 11:55:32: start X-correlation... INFO @ Tue, 14 Jul 2020 11:55:32: end of X-cor INFO @ Tue, 14 Jul 2020 11:55:32: #2 finished! INFO @ Tue, 14 Jul 2020 11:55:32: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 11:55:32: #2 alternative fragment length(s) may be 4,52,525 bps INFO @ Tue, 14 Jul 2020 11:55:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.05_model.r WARNING @ Tue, 14 Jul 2020 11:55:32: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:55:32: #2 You may need to consider one of the other alternative d(s): 4,52,525 WARNING @ Tue, 14 Jul 2020 11:55:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:55:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:55:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:55:34: 2000000 INFO @ Tue, 14 Jul 2020 11:55:40: 3000000 INFO @ Tue, 14 Jul 2020 11:55:46: 4000000 INFO @ Tue, 14 Jul 2020 11:55:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:55:51: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 11:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 11:55:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:55:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:55:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:55:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:55:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.05_summits.bed INFO @ Tue, 14 Jul 2020 11:55:54: Done! pass1 - making usageList (221 chroms): 1 millis pass2 - checking and writing primary data (880 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:55:57: 6000000 INFO @ Tue, 14 Jul 2020 11:55:59: 1000000 INFO @ Tue, 14 Jul 2020 11:56:03: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 11:56:03: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 11:56:03: #1 total tags in treatment: 6884810 INFO @ Tue, 14 Jul 2020 11:56:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:56:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:56:03: #1 tags after filtering in treatment: 6884628 INFO @ Tue, 14 Jul 2020 11:56:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:56:03: #1 finished! INFO @ Tue, 14 Jul 2020 11:56:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:56:04: #2 number of paired peaks: 526 WARNING @ Tue, 14 Jul 2020 11:56:04: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Tue, 14 Jul 2020 11:56:04: start model_add_line... INFO @ Tue, 14 Jul 2020 11:56:04: start X-correlation... INFO @ Tue, 14 Jul 2020 11:56:04: end of X-cor INFO @ Tue, 14 Jul 2020 11:56:04: #2 finished! INFO @ Tue, 14 Jul 2020 11:56:04: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 11:56:04: #2 alternative fragment length(s) may be 4,52,525 bps INFO @ Tue, 14 Jul 2020 11:56:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.10_model.r WARNING @ Tue, 14 Jul 2020 11:56:04: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:56:04: #2 You may need to consider one of the other alternative d(s): 4,52,525 WARNING @ Tue, 14 Jul 2020 11:56:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:56:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:56:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:56:05: 2000000 INFO @ Tue, 14 Jul 2020 11:56:10: 3000000 INFO @ Tue, 14 Jul 2020 11:56:16: 4000000 INFO @ Tue, 14 Jul 2020 11:56:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:56:22: 5000000 INFO @ Tue, 14 Jul 2020 11:56:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:56:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.10_summits.bed INFO @ Tue, 14 Jul 2020 11:56:26: Done! pass1 - making usageList (136 chroms): 0 millis pass2 - checking and writing primary data (364 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:56:28: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:56:33: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 11:56:33: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 11:56:33: #1 total tags in treatment: 6884810 INFO @ Tue, 14 Jul 2020 11:56:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:56:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:56:33: #1 tags after filtering in treatment: 6884628 INFO @ Tue, 14 Jul 2020 11:56:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:56:33: #1 finished! INFO @ Tue, 14 Jul 2020 11:56:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:56:34: #2 number of paired peaks: 526 WARNING @ Tue, 14 Jul 2020 11:56:34: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Tue, 14 Jul 2020 11:56:34: start model_add_line... INFO @ Tue, 14 Jul 2020 11:56:34: start X-correlation... INFO @ Tue, 14 Jul 2020 11:56:34: end of X-cor INFO @ Tue, 14 Jul 2020 11:56:34: #2 finished! INFO @ Tue, 14 Jul 2020 11:56:34: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 11:56:34: #2 alternative fragment length(s) may be 4,52,525 bps INFO @ Tue, 14 Jul 2020 11:56:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.20_model.r WARNING @ Tue, 14 Jul 2020 11:56:34: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:56:34: #2 You may need to consider one of the other alternative d(s): 4,52,525 WARNING @ Tue, 14 Jul 2020 11:56:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:56:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:56:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:56:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:56:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:56:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:56:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521337/SRX8521337.20_summits.bed INFO @ Tue, 14 Jul 2020 11:56:55: Done! pass1 - making usageList (69 chroms): 0 millis pass2 - checking and writing primary data (119 records, 4 fields): 5 millis CompletedMACS2peakCalling